DNA de-novo assembly for plants different than rest organisms?

Question

[chefarov]

Hello all,

I am using cloudbrush de-novo assembler in order to perform assembly on illumina reads from gardenia (plant). Following the same process which is successful for assembling E. Coli raw reads, it fails when I try to assemble on gardenia as I describe here (no useful debugging info).

Thus I was wondering if the procedure of de novo assembly from plants' raw reads differentiates from other organisms, in such a way that an assembler could fail in one case and succeed in the other.

Any thoughts?

Answer 1

[kmcarr00]

The data set you are trying to assemble (http://www.ncbi.nlm.nih.gov/sra/SRR1045129) is transcriptomic (RNA-Seq) data. You can not use this data for genome assembly.

[chefarov]

Thanks kmcarr00,

I can't believe my confusion :P

Answer 2

[lomereiter]

Most likely you've hit memory limit. Plant genomes are different in that they are much larger than bacterial ones (compare ~4.5Gbp of gardenia vs ~4.5Mbp of E.Coli).

[chefarov]

Thanks Iomereiter, I will try to firure it out.